Breast Cancer Cell Lines
In this module, we examine data from experiments with human cancer cell lines from the Physical Sciences in Oncology (PS-ON) Cell Line Characterization Study.
The PS-ON Study includes imaging- and microscopy-based measurements of physical properties of the cells, such as morphology (shape) and motility (movement). We will calculate differential gene expression between two breast cancer cell lines (MDA-MB-231 and T-47D) that migrate at different speeds.
Breast Cancer Cell Lines Activity
For most genes, there is little change in expression between the “fast” and “slow” cell lines. But there are many for which expression is higher in one cell line over the other. These genes are those that appear in the tails of the histogram. The genes with large differential expression are the most interesting to consider because they may provide us with clues as to why the cell lines behave so differently. Let’s find them!
Enriched Biological processes
To test our hypothesis that the genes most differentially expressed are those that contribute to properties associated with cancer, we’ll perform a Gene Ontology analysis of the genes with highest differential expression in the fast versus slow cell line.
The Gene Ontology (GO) Knowledgebase is an easy to use web server for inputting a list of genes and telling us if the genes collectively contribute to particular biological processes versus sets of randomly selected genes. Get the published activity.
